The Pipeline Tools pane enables you to create and manage a customized sequence of operations to automate the processing of a trial.
Pipeline processing is optional, but is useful for automating the data processing operations that you use frequently or on a large number of trials.
The Pipeline Tools pane contains the following sections:
- Available Operations section
The Available Operations section enables you to select the type of pipeline you want to create and the operations to run. Operations are grouped under the following types:
- File Import operations For automating the import of trial files into Vicon Nexus from third-party software packages.
- Core Processing operations For automating reconstruction, labeling, and kinematic fitting to produce 3D trajectories from raw marker data.
- Subject Calibration operations For automating the processing of system and subject calibration.
- Events & Timebar operations For automating operations involving events and/or normally performed using the time bar.
- Fill Gap & Filter Data operations For automating the post-processing of data, such as gap-filling.
- Data Processing operations For automating the production of model outputs (forces and moments, joint angles, etc).
- File Export operations For automating the export of trial files from Nexus to third-party software packages.
- System operations For automating offline camera calibration and applying a codec to video.
- Legacy operations For automating the processing of legacy trial data.
Current Pipeline section
At the top of the Current Pipeline section, the configuration management controls enable you to create or manage configurations for the settings specified in the Pipeline Tools pane.
The middle of the Current Pipeline section enables you to manage the pipeline operations and view their status with the playback controls and progress bar.
In the list at the bottom of the Current Pipeline section, you can view the operations included in the currently loaded pipeline.
For information on using pipelines, see Work with pipelines in the Vicon Nexus User Guide.
Pipeline operations are run in the order they appear in this list. You can drag operations into the desired position in the list. Alternatively, you can run an individual operation by right-clicking on it and clicking Run selected Op.
- Properties pane
You can view or change settings for the selected pipeline operation in the Properties pane at the bottom of the Pipeline Tools pane.
Pipeline operations are found in the Pipeline Tools pane, in the Available Operations section.
File Import operations
Use File Import operations to automate the import of trial files to Vicon Nexus from third-party software packages.
Import a video .avi file to be saved and associated with the current trial.
Import subject parameters specified in a .mp file into the active subject.
Import a labeling skeleton (.vsk) file.
Import a calibration file (.xcp) into the current trial to replace the current calibration.
Core Processing operations
Use Core Processing operations to automate the processing of offline reconstruction, labeling, and kinematic fitting to produce 3D trajectories from raw marker data.
Performs one or more of: reconstruction, labeling, and subject motions. Running this operation is faster than running each process individually.
3D trajectories are reconstructed from the raw 2D marker data.
Controls how 3D trajectories are labeled with subject data
Controls how the labeling skeleton contained in the .vsk is kinematic-fitted to the marker data. In addition to specifying the frames on which to operate, you can adjust settings for:
The equivalent settings for Live processing can be found in the Local Vicon System properties, found in the System Resources pane.
Subject Calibration operations
Use Subject Calibration operations to automate the processing of labeling skeleton calibration.
Set Autolabel Pose
Sets the pose for Autolabel Static to be the pose at the selected frame.
Run on a reconstructed static trial to automatically label the labeling skeleton in a single frame, using information from the .vst file. It matches the shape of the reconstruction to the shape of the subject template for that pose.
Scale Subject VSK
Scales the labeling skeleton to be the same size as a labeled set of reconstructions on a particular frame. The scale factor is calculated assuming that the subject is in the same pose as was used for Autolabel Static (see above).
Functional Skeleton Calibration
Calibrate the subject's bone lengths, joint locations, and marker locations from a whole trial. Use to calibrate a whole ROM trial.
Functional Skeleton Calibration - Markers-only
Calibrate the subject's marker locations from a whole trial. This is useful, for example if a marker becomes detached from the subject and you need to re-run the calibration with the replaced marker.
Static Skeleton Calibration
Calibrate the subject's bone lengths, joint locations, and marker locations from a single frame. Use to calibration a static calibration, as in versions of Vicon Nexus earlier than 2.0.
Static Skeleton Calibration - Markers-only
Uses a single frame to update the marker locations for the labeling skeleton. This operation both fits the subject pose (that is, the pose that was defined when the labeling skeleton was created) to the labeled reconstructions and calibrates the marker locations.
|Update Skeleton Parameters|
Initial label booting can be improved by providing more representative data from a movement or ROM trial. This operation enables you to do this by updating the default values of a selected skeleton with movement or ROM trial data contained in the current calibrated labeling skeleton (VSK). The options for this operation are:
Calculate Skeleton Joint & Marker Statistics
Measure the subject's labeling statistics from a whole trial.
Finds the Optimum Common Shape
Calibrate joint positions using the Symmetrical Center of Rotation Estimation and Symmetrical Axis of Rotation Analysis.
For more information on the labeling skeleton calibration operations, see Labeling skeleton calibration in detail.
Events & Timebar operations
Use Events & Timebar operations to automate processes relating to events and the timebar.
Auto Crop Trial
For trials where the subject starts outside the volume, moves into the volume and then exits, Nexus can automatically determine the first and last frame where the subject is fully in the volume.
Based on user-defined parameters, this operation detects the pattern of the tracked marker at the set events and defines these events for the rest of the trial. The available parameters are: marker being tracked; the X, Y, or Z component of the marker; and the position, velocity, or acceleration of the marker. Normally used after the Detect Events from Forceplate operation.
Detect Events from ForcePlate
Automatically detects gait cycle events and adds them to the time bar throughout the trial using vertical GRFs measured by a force plate connected to the Vicon system. Includes the option to set the force threshold and the label of the markers attached to the front and back of the foot for both sides.
Delete Timebar Events
Delete events from the specified range for the subject(s). An advanced option lets you choose whether to delete events that are inside or outside the specified range of frames.
Fill Gap & Filter Data operations
Use Fill Gap & Filter Data operations to automate gap-filling and other post-processing.
Fill Gaps - Cyclic
For trials that contain captured data that is cyclic in nature (for example, when a motion on a treadmill or other repetitive motion is captured), fills gaps using patterns from earlier or later gait cycles. You can specify the Gap Length, Units, First and Last Frame, and select the trajectories to fill.
Fill Gaps - Kinematic
Fills all gaps in trajectories that pass through a selected segment, based on calculated kinematics. To run this operation, you must have already obtained the kinematic data on which to base gap-filling, for example, by running the Nexus Legacy Fit Motion pipeline.
Fill Gaps - Pattern
Fills the selected gap using the shape of another trajectory without a gap. Use this tool only if there is a suitable marker with a trajectory similar to the one whose gap you wish to fill.
Fill Gaps - Rigid Body
Fills gaps in a trajectory based on other trajectories in a rigid body. This option is the Nexus equivalent of the Replace 4 option, which is available in BodyBuilder. Use this option when a rigid or semi-rigid relationship exists between markers.
Fill Gaps - Woltring
Run on labeled dynamic trials to fill in gaps using Woltring quintic spline interpolation. Includes the option to choose maximum gap frame length to fill.
You can configure the following settings in the Properties section:
Filter Analog Data - Butterworth
Filter analog device data using a low-pass digital Butterworth filter. The filter is by default setup as recommended in Winter, D.A. Biomechanics of Motor Control and Human Movement to filter out signal noise above 300 Hz using a fourth order filter with zero lag (see descriptions below for an explanation of these parameters).
Filter Model Outputs - Butterworth
Filter subject model outputs using a low-pass digital Butterworth filter. The filter is by default setup as recommended in Winter, D.A. Biomechanics of Motor Control and Human Movement to filter out signal noise above 6 Hz using a Fourth Order filter with zero lag.
Filter Trajectories - Butterworth
Filter trajectories using a low-pass digital Butterworth filter. The filter is by default set up as recommended in Winter, D.A. Biomechanics of Motor Control and Human Movement to filter out signal noise above 6 Hz using a Fourth Order filter with zero lag.
Filter Trajectories - VCM Spline
Vicon Gait Model event VCM Spline Filter
Filter Trajectories - Woltring
Filters the data using the Woltring filter to ensure smooth trajectories for calculating kinetics.
Delete Optional Subject Marker
Run on a any trial to delete a specified group of subject markers from the marker list that will not be used during the dynamic captures.
Delete Unlabeled Trajectories
Run on a fully labeled trial to delete any remaining unlabeled trajectories. Includes the option to choose maximum length of unlabeled trajectory to delete.
Data Processing operations
Use Processing operations to automate real-time and offline motion capture data processing.
Process Static Plug-in Gait Model
Runs the static Plug-In Gait model on the active subject of the current trial.
Calculate Gait Cycle Parameters
Calculate Vicon Gait Model temporal parameters. Includes the option to set the output units.
Process Dynamic Plug-in Gait Model
Runs the dynamic Plug-In Gait model on the active subject of the current trial.
Run Static BodyLanguage Model
Runs the static BodyLanguage model
Run Static Oxford Foot Model
Runs the static Oxford Foot Model pipeline operation (installed as part of Nexus) that was previously available as a separate legacy VPI.
Run Dynamic BodyLanguage Model
Runs the dynamic BodyLanguage model
Run Dynamic Oxford Foot Model
Runs the dynamic Oxford Foot Model pipeline operation (installed as part of Nexus) that was previously available as a separate legacy VPI.
Run MatLab Operation
Execute MATLAB script.
For information on using MATLAB with Nexus, see Modeling with MATLAB.
|Run ProCalc Operation|
Run ProCalc scripts/models directly from Nexus.
For information on Procalc, see the Vicon Procalc documentation.
|Run Python Operation|
Execute Python script.
For information on using Python with Nexus, see Modeling with Python.
Finds the coordinate system trace using the Optimum Common Shape Technique.
For more information, see Biomechanics workflow.
Process SCoRE / SARA
Generates joint position model outputs using Symmetrical Center of Rotation Estimation and Symmetrical Axis of Rotation Analysis.
For more information, see Biomechanics workflow.
|Calculate Gait Deviation Index|
Generates a GDI (Gait Deviation Index) score for the subject of the current trial.1
When you run this operation on a trial, two GDI values (left and right), are output to the log and saved as subject parameters.
To output these values when you run the Export ASCII pipeline operation, select the Export Gait Cycle Parameters option.
Delete Model Outputs
Enables you to delete from the current trial the selected model output(s), all model outputs, or to specify a comma-separated list of model output names.
The following research publication provides supporting information on the scientific basis and validation of Vicon's implementation of the calculation of the GDI score:
SCHWARTZ, M. H., and ROZUMALSKI, A., The gait deviation index: A new comprehensive index of gait pathology, Gait & Posture 28 (2008), p351–357.
File Export operations
Use File Export operations to export of data from Vicon Nexus for use with third-party software packages.
Export 3D Overlay Video
Export a copy of the reference video .avi file(s) with the 3D Perspective data overlaid onto the video image. You can choose which 3D view option to display and select the codec used to compress the new .avi file.
You can configure the following settings in the Properties section:
Tip: If you want to export labeled subjects in the Nexus 3D workspace, use instead the Export Workspace to AVI button (available on the View pane toolbar) . For more information, see Export 3D Workspace as AVI in the Vicon Nexus User Guide.
Export delimited ASCII format to a .csv or .txt file, or another format that you specify by clearing the Macro check box (click the downward arrow at the right of the extension list) and entering the required extension. You can select commas, tabs, or line feeds as the delimiter.
Export the current state of the processed data to a .c3d file. You can then import the data into other software for further processing or report generation. For example, in Vicon Polygon you can visualize the trajectories, kinematic model elements, and kinetics data.
If you manually import the corresponding .vst file into Polygon, it also visualizes the bones.
Export an .mkr file. You can choose whether the exported file name is based on the active subject name(s) or active labeling skeleton template name(s). If you choose Active Labeling Skeleton Names, the name of any labeling skeleton template attached to the subject (for example, PlugInGait FullBody Ai) is used as the name of the MKR file. If more than one subject is present with the same model attached, a log message indicates that only one MKR file will be exported.
Export Nexus data files in .mox format for MoXie
Export the current subject parameters to an .mp file (subject parameter file compatible with legacy software).
Export a .trc file.
Export a labeling skeleton (.vsk) file
Export the current calibration file to an .xcp file in a specified location.
|Export MOT||Export files in .mot format for use in OpenSim.|
Save Trial - C3D + VSK
Save the files associated with the currently open trial.
For more information on how to use the export operations, see Export trial data in the Vicon Nexus User Guide.
Use System operations to automate oflline camera calibration and applying codecs to video files.
Process Offline Camera Calibration
Run on a captured trial of a calibration wand wave to calibrate a system (instead of calibrating the system live).
Transcode Video for Trial
Automates transcoding the raw video files associated with the current trial. Enables you to choose the required codec.
Apply Codec to Video
Applies a codec to all AVIs associated with the current trial. You can select which codec to use, whether to keep the original movie file, and whether to remove interlacing.
Important: Reverting to the backup file to re-do the de-interlacing is not supported in Nexus. For more information, see De-interlace AVI files in the Vicon Nexus User Guide.
Reset force plate offsets
Resets the force plate offsets. Enables you to specify the range of frames on which to operate, the affected device(s), and the range of frames to use for zeroing the force plate.
Set Camera Calibration Origin
Sets the camera calibration origin using a calibration object.
Use Legacy operations to automate the processing of legacy trial data:
Nexus Legacy Labeler
Run on fully reconstructed trials to label the subject as a whole instead of frame-by-frame as in the Core Processor. This operation requires a .vsk file.
Nexus Legacy Fit Motion
Run on fully labeled trials to Kinematic Fit the trial as a whole instead of frame-by-frame as in the Core Processor.